rs6882716

Positions:

• chr5-10797774-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.786 in 152,120 control chromosomes in the GnomAD database, including 48,954 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (48954 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119500 AN: 152002 Hom.: 48934 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.786

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.786 AC: 119561 AN: 152120 Hom.: 48954 Cov.: 32 AF XY: 0.778 AC XY: 57864 AN XY: 74384

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.778

Alfa AF: 0.844 Hom.: 13117

Bravo AF: 0.769

Asia WGS AF: 0.419 AC: 1459 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6882716; hg19: chr5-10797886;